Tutorial for SameSpots v4.5
Using this tutorial, you will learn the basic workflow of analysis within SameSpots. Although it will not go into depth on the various features, it will help you become familiar with the steps required to identify the interesting spots in your experiments.
The data used for the tutorial is taken from a DIGE experiment; if you don't normally use DIGE, there's also a single-stain tutorial available.
About the experiment
The data you'll use in this tutorial is a subset of gel images from a study into the effects of three different drug candidates. It consists of 12 images, taken from a total of 4 DIGE gels, each gel running 2 experimental samples (cy3- and cy5-stained) and an internal standard (cy2).
Consequently, each condition under test — control, treated with Drug A, treated with Drug B, or treated with Drug C — is represented here by only 2 replicates. It's important to note that this is not recommended for real-world experiments. We've used a small dataset here to keep the download size to a minimum, while still allowing us to demonstrate the key features of the software.
For more information on choosing replicate numbers for your own experiments, please see the advice on the Fixing Proteomics Campaign website.
Before you start…
In SameSpots, the first step of any analysis is to create an experiment file and import the gel images into it. For this tutorial, the images are packaged in a separate installation program, which can be downloaded here:
SameSpots DIGE Tutorial.exe (30MB)
Once downloaded, run the file and choose a folder into which the gel images will be copied and click the Copy button.
Creating the experiment
- Click the New button, at the bottom-left, to create a new experiment
- In the New Experiment window, enter the name SameSpots tutorial in the text entry box
- Select the DIGE with internal standards option
- Click the Create button to create the new experiment
SameSpots then opens the new experiment, putting us at the start of the main analysis workflow, ready to import our gel images. Let's get started…